From d38b6ffa0b86e0ea252ba752aebdf19551920062 Mon Sep 17 00:00:00 2001
From: Matti Pellika <matti.pellikka@tut.fi>
Date: Fri, 1 Jan 2010 17:43:34 +0000
Subject: [PATCH] Changed homology generator chain mesh element orientations
(determined by vertex order) so that post-processing data isn't needed to
save the generators, instead all the elements have coefficient 1 now in the
chain. Due to this also reverted changes made to GModel writeMSH method in my
earlier commit (they became obsolete).
---
Geo/ChainComplex.cpp | 11 +++++---
Geo/GModel.h | 3 ++-
Geo/GModelIO_Mesh.cpp | 54 ++++++++++++++++++--------------------
Geo/Homology.h | 5 ++--
Post/PViewDataGModelIO.cpp | 2 +-
tutorial/t10.geo | 8 +++---
6 files changed, 45 insertions(+), 38 deletions(-)
diff --git a/Geo/ChainComplex.cpp b/Geo/ChainComplex.cpp
index 1e32afa678..d9a522cb7d 100644
--- a/Geo/ChainComplex.cpp
+++ b/Geo/ChainComplex.cpp
@@ -871,18 +871,22 @@ void Chain::createPView(){
std::vector<MElement*> elements;
MElementFactory factory;
-
std::map<int, std::vector<double> > data;
for(citer cit = _cells.begin(); cit != _cells.end(); cit++){
Cell* cell = (*cit).first;
int coeff = (*cit).second;
std::vector<MVertex*> v = cell->getVertexVector();
+ if(cell->getDim() > 0 && coeff == -1){ // flip orientation
+ MVertex* temp = v[0];
+ v[0] = v[1];
+ v[1] = temp;
+ }
MElement *e = factory.create(cell->getTypeForMSH(), v, cell->getNum(), cell->getPartition());
elements.push_back(e);
- std::vector<double> coeffs (1,coeff);
- data.insert(std::make_pair(e->getNum(), coeffs));
+ std::vector<double> coeffs (1,1);
+ data[e->getNum()] = coeffs;
}
int max[4];
@@ -903,6 +907,7 @@ void Chain::createPView(){
_model->storeChain(getDim(), entityMap, physicalMap);
_model->setPhysicalName(getName(), getDim(), physicalNum);
+ // only for visualization
if(!data.empty()) PView *chain = new PView(getName(), "ElementData", getGModel(), data, 0, 1);
return;
diff --git a/Geo/GModel.h b/Geo/GModel.h
index 2346ff5c4c..a71531f51e 100644
--- a/Geo/GModel.h
+++ b/Geo/GModel.h
@@ -371,7 +371,7 @@ class GModel
// Gmsh mesh file format
int readMSH(const std::string &name);
int writeMSH(const std::string &name, double version=1.0, bool binary=false,
- bool saveAll=false, bool saveParametric=false, double scalingFactor=1.0, bool eleRenumbering=true);
+ bool saveAll=false, bool saveParametric=false, double scalingFactor=1.0);
int writeDistanceMSH(const std::string &name, double version=1.0, bool binary=false,
bool saveAll=false, bool saveParametric=false, double scalingFactor=1.0);
@@ -448,6 +448,7 @@ class GModel
std::map<int, std::map<int, std::string> > &physicalMap){
_storeElementsInEntities(entityMap);
_storePhysicalTagsInEntities(dim, physicalMap);
+ _associateEntityWithMeshVertices();
}
};
diff --git a/Geo/GModelIO_Mesh.cpp b/Geo/GModelIO_Mesh.cpp
index edff2d5d6d..4c14ba50ae 100644
--- a/Geo/GModelIO_Mesh.cpp
+++ b/Geo/GModelIO_Mesh.cpp
@@ -529,16 +529,14 @@ static void writeElementHeaderMSH(bool binary, FILE *fp, std::map<int,int> &elem
template<class T>
static void writeElementsMSH(FILE *fp, T *ele, bool saveAll,
double version, bool binary, int &num, int elementary,
- std::vector<int> &physicals, int parentNum, bool eleRenumbering=true)
+ std::vector<int> &physicals, int parentNum)
{
if(saveAll){
- if(eleRenumbering) ele->writeMSH(fp, version, binary, ++num, elementary, 0, parentNum);
- else ele->writeMSH(fp, version, binary, 0, elementary, 0, parentNum);
+ ele->writeMSH(fp, version, binary, ++num, elementary, 0, parentNum);
}
else{
for(unsigned int j = 0; j < physicals.size(); j++){
- if(eleRenumbering) ele->writeMSH(fp, version, binary, ++num, elementary, physicals[j], parentNum);
- else ele->writeMSH(fp, version, binary, 0, elementary, physicals[j], parentNum);
+ ele->writeMSH(fp, version, binary, ++num, elementary, physicals[j], parentNum);
}
}
}
@@ -546,24 +544,24 @@ static void writeElementsMSH(FILE *fp, T *ele, bool saveAll,
template<class T>
static void writeElementsMSH(FILE *fp, std::vector<T*> &ele, bool saveAll,
double version, bool binary, int &num, int elementary,
- std::vector<int> &physicals, bool eleRenumbering=true)
+ std::vector<int> &physicals)
{
for(unsigned int i = 0; i < ele.size(); i++)
writeElementsMSH(fp, ele[i], saveAll, version, binary, num,
- elementary, physicals, 0, eleRenumbering);
+ elementary, physicals, 0);
}
template<class T>
static void writeElementsMSH(FILE *fp, std::vector<T*> &ele, bool saveAll,
double version, bool binary, int &num, int elementary,
- std::vector<int> &physicals, std::map<MElement *, int> &parentsNum, bool eleRenumbering=true)
+ std::vector<int> &physicals, std::map<MElement *, int> &parentsNum)
{
for(unsigned int i = 0; i < ele.size(); i++) {
int parentNum = (ele[i]->getParent() != NULL &&
parentsNum.find(ele[i]->getParent()) != parentsNum.end()) ?
parentsNum.find(ele[i]->getParent())->second : 0;
writeElementsMSH(fp, ele[i], saveAll, version, binary, num,
- elementary, physicals, parentNum, eleRenumbering);
+ elementary, physicals, parentNum);
}
}
int GModel::writeDistanceMSH(const std::string &name, double version, bool binary,
@@ -658,7 +656,7 @@ int GModel::writeDistanceMSH(const std::string &name, double version, bool binar
}
int GModel::writeMSH(const std::string &name, double version, bool binary,
- bool saveAll, bool saveParametric, double scalingFactor, bool eleRenumbering)
+ bool saveAll, bool saveParametric, double scalingFactor)
{
FILE *fp = fopen(name.c_str(), binary ? "wb" : "w");
if(!fp){
@@ -794,99 +792,99 @@ int GModel::writeMSH(const std::string &name, double version, bool binary,
writeElementHeaderMSH(binary, fp, elements, MSH_PNT);
for(viter it = firstVertex(); it != lastVertex(); ++it)
writeElementsMSH(fp, (*it)->points, saveAll, version, binary, num,
- (*it)->tag(), (*it)->physicals, eleRenumbering);
+ (*it)->tag(), (*it)->physicals);
writeElementHeaderMSH(binary, fp, elements, MSH_LIN_2, MSH_LIN_3, MSH_LIN_4,
MSH_LIN_5);
for(eiter it = firstEdge(); it != lastEdge(); ++it)
writeElementsMSH(fp, (*it)->lines, saveAll, version, binary, num,
- (*it)->tag(), (*it)->physicals, eleRenumbering);
+ (*it)->tag(), (*it)->physicals);
writeElementHeaderMSH(binary, fp, elements, MSH_TRI_3, MSH_TRI_6, MSH_TRI_9,
MSH_TRI_10, MSH_TRI_12, MSH_TRI_15, MSH_TRI_15I, MSH_TRI_21);
for(itP = parents[0].begin(); itP != parents[0].end(); itP++)
if(itP->first->getType() == TYPE_TRI) {
writeElementsMSH(fp, itP->first, saveAll, version, binary, num,
- itP->second->tag(), itP->second->physicals, 0, eleRenumbering);
+ itP->second->tag(), itP->second->physicals, 0);
parentsNum[itP->first] = num;
}
for(fiter it = firstFace(); it != lastFace(); ++it)
writeElementsMSH(fp, (*it)->triangles, saveAll, version, binary, num,
- (*it)->tag(), (*it)->physicals, eleRenumbering);
+ (*it)->tag(), (*it)->physicals);
writeElementHeaderMSH(binary, fp, elements, MSH_QUA_4, MSH_QUA_9, MSH_QUA_8,
MSH_QUA_16, MSH_QUA_25, MSH_QUA_36, MSH_QUA_12, MSH_QUA_16I,
MSH_QUA_20);
for(itP = parents[0].begin(); itP != parents[0].end(); itP++)
if(itP->first->getType() == TYPE_QUA) {
writeElementsMSH(fp, itP->first, saveAll, version, binary, num,
- itP->second->tag(), itP->second->physicals, 0, eleRenumbering);
+ itP->second->tag(), itP->second->physicals, 0);
parentsNum[itP->first] = num;
}
for(fiter it = firstFace(); it != lastFace(); ++it)
writeElementsMSH(fp, (*it)->quadrangles, saveAll, version, binary, num,
- (*it)->tag(), (*it)->physicals, eleRenumbering);
+ (*it)->tag(), (*it)->physicals);
writeElementHeaderMSH(binary, fp, elements, MSH_POLYG_);
for(itP = parents[0].begin(); itP != parents[0].end(); itP++)
if(itP->first->getType() == TYPE_POLYG) {
writeElementsMSH(fp, itP->first, saveAll, version, binary, num,
- itP->second->tag(), itP->second->physicals, 0, eleRenumbering);
+ itP->second->tag(), itP->second->physicals, 0);
parentsNum[itP->first] = num;
}
for(fiter it = firstFace(); it != lastFace(); it++)
writeElementsMSH(fp, (*it)->polygons, saveAll, version, binary, num,
- (*it)->tag(), (*it)->physicals, parentsNum, eleRenumbering);
+ (*it)->tag(), (*it)->physicals, parentsNum);
writeElementHeaderMSH(binary, fp, elements, MSH_TET_4, MSH_TET_10, MSH_TET_20,
MSH_TET_35, MSH_TET_56, MSH_TET_52);
for(itP = parents[1].begin(); itP != parents[1].end(); itP++)
if(itP->first->getType() == TYPE_TET) {
writeElementsMSH(fp, itP->first, saveAll, version, binary, num,
- itP->second->tag(), itP->second->physicals, 0, eleRenumbering);
+ itP->second->tag(), itP->second->physicals, 0);
parentsNum[itP->first] = num;
}
for(riter it = firstRegion(); it != lastRegion(); ++it)
writeElementsMSH(fp, (*it)->tetrahedra, saveAll, version, binary, num,
- (*it)->tag(), (*it)->physicals, eleRenumbering);
+ (*it)->tag(), (*it)->physicals);
writeElementHeaderMSH(binary, fp, elements, MSH_HEX_8, MSH_HEX_27, MSH_HEX_20);
for(itP = parents[1].begin(); itP != parents[1].end(); itP++)
if(itP->first->getType() == TYPE_HEX) {
writeElementsMSH(fp, itP->first, saveAll, version, binary, num,
- itP->second->tag(), itP->second->physicals, 0, eleRenumbering);
+ itP->second->tag(), itP->second->physicals, 0);
parentsNum[itP->first] = num;
}
for(riter it = firstRegion(); it != lastRegion(); ++it)
writeElementsMSH(fp, (*it)->hexahedra, saveAll, version, binary, num,
- (*it)->tag(), (*it)->physicals, eleRenumbering);
+ (*it)->tag(), (*it)->physicals);
writeElementHeaderMSH(binary, fp, elements, MSH_PRI_6, MSH_PRI_18, MSH_PRI_15);
for(itP = parents[1].begin(); itP != parents[1].end(); itP++)
if(itP->first->getType() == TYPE_PRI) {
writeElementsMSH(fp, itP->first, saveAll, version, binary, num,
- itP->second->tag(), itP->second->physicals, 0, eleRenumbering);
+ itP->second->tag(), itP->second->physicals, 0);
parentsNum[itP->first] = num;
}
for(riter it = firstRegion(); it != lastRegion(); ++it)
writeElementsMSH(fp, (*it)->prisms, saveAll, version, binary, num,
- (*it)->tag(), (*it)->physicals, eleRenumbering);
+ (*it)->tag(), (*it)->physicals);
writeElementHeaderMSH(binary, fp, elements, MSH_PYR_5, MSH_PYR_14, MSH_PYR_13);
for(itP = parents[1].begin(); itP != parents[1].end(); itP++)
if(itP->first->getType() == TYPE_PYR) {
writeElementsMSH(fp, itP->first, saveAll, version, binary, num,
- itP->second->tag(), itP->second->physicals, 0, eleRenumbering);
+ itP->second->tag(), itP->second->physicals, 0);
parentsNum[itP->first] = num;
}
for(riter it = firstRegion(); it != lastRegion(); ++it)
writeElementsMSH(fp, (*it)->pyramids, saveAll, version, binary, num,
- (*it)->tag(), (*it)->physicals, eleRenumbering);
+ (*it)->tag(), (*it)->physicals);
writeElementHeaderMSH(binary, fp, elements, MSH_POLYH_);
for(itP = parents[1].begin(); itP != parents[1].end(); itP++)
if(itP->first->getType() == TYPE_POLYH) {
writeElementsMSH(fp, itP->first, saveAll, version, binary, num,
- itP->second->tag(), itP->second->physicals, 0, eleRenumbering);
+ itP->second->tag(), itP->second->physicals, 0);
parentsNum[itP->first] = num;
}
for(riter it = firstRegion(); it != lastRegion(); ++it)
writeElementsMSH(fp, (*it)->polyhedra, saveAll, version, binary, num,
- (*it)->tag(), (*it)->physicals, parentsNum, eleRenumbering);
+ (*it)->tag(), (*it)->physicals, parentsNum);
if(binary) fprintf(fp, "\n");
diff --git a/Geo/Homology.h b/Geo/Homology.h
index 57786ec3b2..b1a29f0db4 100644
--- a/Geo/Homology.h
+++ b/Geo/Homology.h
@@ -108,13 +108,14 @@ class Homology
// write the generators to a file
bool writeGeneratorsMSH(std::string fileName, bool binary=false){
- if(!_model->writeMSH(fileName, 2.0, binary, false, false, 1.0, false)) return false;
+ if(!_model->writeMSH(fileName, 2.0, binary)) return false;
+ /*
for(int i = 0; i < 4; i++){
for(int j = 0; j < _generators[i].size(); j++){
Chain* chain = _generators[i].at(j);
if(!chain->writeChainMSH(fileName)) return false;
}
- }
+ }*/
Msg::Info("Wrote results to %s.", fileName.c_str());
printf("Wrote results to %s. \n", fileName.c_str());
diff --git a/Post/PViewDataGModelIO.cpp b/Post/PViewDataGModelIO.cpp
index 48304312c7..ac55cda4d5 100644
--- a/Post/PViewDataGModelIO.cpp
+++ b/Post/PViewDataGModelIO.cpp
@@ -117,7 +117,7 @@ bool PViewDataGModel::writeMSH(std::string fileName, bool binary)
GModel *model = _steps[0]->getModel();
- if(!model->writeMSH(fileName, 2.0, binary, false, false, 1.0, false)) return false;
+ if(!model->writeMSH(fileName, 2.0, binary)) return false;
// append data
FILE *fp = fopen(fileName.c_str(), binary ? "ab" : "a");
diff --git a/tutorial/t10.geo b/tutorial/t10.geo
index 0335ebc0b3..bd92364cc0 100644
--- a/tutorial/t10.geo
+++ b/tutorial/t10.geo
@@ -6,7 +6,10 @@
*
*********************************************************************/
-// Homology computation in Gmsh finds representatives of (relative) homology spaces using a mesh of a model. Those representatives generate the (relative) homology spaces of the model. Alternativelly, Gmsh can only look for the ranks of the (relative) homology spaces, the Betti numbers of the model.
+// Homology computation in Gmsh finds representative chains of (relative) homology spaces using a mesh of a model. Those representatives generate the (relative) homology spaces of the model. Alternatively, Gmsh can only look for the ranks of the (relative) homology spaces, the Betti numbers of the model.
+
+// The generators chains are stored in a given .msh-file as physical groups, whose mesh elements are oriented such that their coeffecients are 1 in the generator chain.
+
// Create an example geometry
@@ -137,13 +140,12 @@ HomCut("t10_homcut.msh") = {{69}, {70, 71, 72, 73}};
// Only find and print the ranks of the relative homology spaces (Betti numbers).
HomRank {{69},{70, 71, 72, 73}};
-// Hide mesh elements
+// Hide mesh elements for instant visualization
Mesh.Points = 0;
Mesh.Lines = 0;
Mesh.Triangles = 0;
Mesh.Tetrahedra = 0;
-
// More examples (uncomment):
// HomGen("t10_homgen.msh_1") = {{69}, {}};
// HomGen("t10_homgen.msh_2") = {{69}, {74}};
--
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